Curr. Issues Mol. Biol. (2000) 2(3): 71-85.
Introductory Experiments 71
Introductory Experiments in Recombinant DNA
Robert C. Tait*
2318 Cezanne Court, Davis, CA 95616, USA
Abstract
Nine practical exercises demonstrate the basic
principles in recombinant DNA. The exercises explain
the principles that DNA equals genes and that changes
in DNA cause changes in genetic properties. The aim
is to provide a teaching resource that can be used to
illustrate the theory and applications of molecular
biology to highschool students, undergraduate
students, medics, dentists, doctors, nurses, life
scientists, and anyone learning the basics of DNA
technology.
Introduction
The exercises contained in this article have been chosen
to demonstrate the basic principles in recombinant DNA:
digestion of DNA with a restriction endonuclease, gel
electrophoresis of DNA samples, insertion of DNA into cells
can change their growth characteristics, and DNA can be
rearranged to cause changes in genetic properties. The
exercises are intended to be an example of the principles
that DNA equals genes and that changes in DNA cause
changes in genetic properties.
Each exercise is preceded by a short discussion of
the principles involved and the specific goals of the
procedure. Solutions that must be prepared for each
exercise are detailed in a Materials section. While some
of these “recipes” can be changed considerably without
affecting the outcome of the exercise, many of the “minor”
details are crucial to the success of the protocol. For
example, a restriction digestion buffer may contain only 6
mM NaCl relative to 50 mM TRIS-Cl buffer, an apparently
trivial amount of salt in the overall scheme of things.
However, many enzymes are very specific about salt
concentrations required for activity, and deleting the NaCl
from the buffer may inactivate or actually change the
recognition properties of the enzyme. Please do not
arbitrarily change recipes and expect exercises to work
properly.
The recipes assume a simple knowledge of chemistry
and use standard abbreviations regarding concentrations:
M = moles/liter = molar
mM = millimoles/liter = 10 -3 moles/liter = millimolar
l = liter
ml = milliliter = 10 -3 liter
µl = microliter = 10 -6 liter
When pH of a solution is indicated, there is generally an
allowance of about 0.5 pH unit. If a pH of 7.5 is indicated,
a pH of 7.0 to 8.0 will generally suffice. If possible, use a
pH meter in the preparation of solutions, otherwise, use
pH paper and be as accurate as reasonable.
© 2000 Caister Academic Press
The instructions often require the addition of water,
sometimes indicated specifically as distilled water (dH2O).
For electrophoresis, media, and general solutions, tap
water will often suffice. For reactions involving enzymes,
distilled water should always be used rather than tap water.
Many enzymes can be inhibited by heavy metal salts
present at low levels in tap water. Distilled water purchased
for use in a steam iron can be used in the event that there
is no access to a water still or deionizer.
Certain solutions must be sterilized (media for culture
of bacteria, for example). An electric hot plate and a
standard pressure cooker can be used as a substitute for
an autoclave. Heat media at 16 lb pressure for 20-30
minutes to sterilize small volumes of liquids (less than 500
ml solution per container). While a microwave oven is used
for melting agarose in nearly every molecular biology
research lab, a hot plate with a boiling water bath or a gas
burner will accomplish the same thing. Agarose solutions
have a tendency to superheat and boil violently when the
agarose granules are first melting. A solution of agarose
that has been previously melted, then allowed to cool and
solidify is less likely to boil violently when melted the second
time.
As a note of caution, realize that molecular biology
uses a number of noxious chemicals: organic solvents
(phenol, chloroform, ether) are quite toxic and certain
compounds (ethidium bromide and UV light, for example)
are known mutagens capable of causing genetic changes.
The use of such compounds has been kept to a minimum
in these exercises and where such compounds are used,
precautions are noted in directions for the exercises. During
electrophoresis, although low voltages are used, severe
injury is possible. Electrophoresis boxes should have an
interlock mechanism - a device that prevents the current
from being applied to the buffer when the buffer is exposed.
Most commercial gel boxes include this safety design
feature, as do the plans that accompany these exercises.
COMMON SENSE IS REQUIRED IN ALL LAB
EXERCISES. Food and drinks should be prohibited from
the work area and lab coats should be worn. Power units
should be turned off while loading gels or handling gel
boxes. All spills should be cleaned up when they occur.
Having previously indicated that these exercises
should not be arbitrarily altered, I now emphasize that these
protocols should not be considered inviolate. There are
about 113 ways to accomplish the same thing in any
molecular biology exercise. As your understanding of these
methods increases, you will recognize how protocols can
be altered to suit a particular circumstance. Other protocols
will appear that seem easier or more reproducible in your
own situation. While this is one of the aspects of molecular
biology that makes the methods so powerful, this variability
also tends to unnecessarily confuse novices in the field.
Before modifying a protocol, be certain that you understand
the changes and that these alterations will not adversely
affect the outcome of an exercise.
The bacteriophage lambda, pBR322, and pUC19
plasmid DNA samples used in these exercises are available
from a number of commercial suppliers. The bacterial DNA
*Corresponding author
72 Tait
can be prepared by a simple procedure (see Appendix)
that uses detergent lysis and phenol/chloroform extraction
to prepare high quality DNA. Commercially available calf
thymus DNA can be substituted. Plasmid recombinants
containing E. coli DNA in pUC19 were chosen specifically
to work entirely with bacterial DNA and minimize any
misperception of biohazard potential. Competent cells are
commercially available from several sources, but
acceptable competent cells can also be prepared with a
minimum of expertise.
Exercise 1. Gel electrophoresis of nucleic acids
Nucleic acid samples are often subjected to gel
electrophoresis to characterize the size and number of
different fragments in the sample. In this exercise, DNA
samples that have been digested with restriction enzymes
and mixed with a tracking dye will be subjected to agarose
gel electrophoresis. The electrophoresis buffer, the salt
solution that both conducts electric current and controls
the pH of the solution during the separation of the DNA
fragments, is TRIS/borate/EDTA or TBE, a commonly used
buffer system.
When charged molecules are placed in an electric field,
the molecules will migrate towards one of the electrodes,
depending on the net charge of the molecule. Nucleic acids
have an overall negative charge due to the negative
charges associated with the phosphate backbone of the
molecules, so they will migrate towards the positive
electrode. Since the distribution of phosphate is very regular
across the length of the nucleic acid molecule, nucleic acids
have a constant charge/mass ratio and will therefore
migrate at the same rate in an electric field.
Separation of nucleic acid molecules of different size
or conformation is achieved by adding a support matrix to
the electric field and forcing the molecules to migrate
through this matrix, typically agarose or polyacrylamide gel.
This matrix acts like a sieve that allows small molecules to
go faster than large molecules. The result is that molecules
separate in the matrix according to their relative size and
shape.
This exercise will use gel electrophoresis to examine
the fragments present in several DNA samples. The
principle goal is to obtain experience in pouring gels,
loading DNA samples, and visualizing the DNA bands.
Due to the small volumes of sample to be applied to
the gel, samples are routinely handled with a manual
micropipet device that uses a disposable plastic tip to
handle a 10 to 20 µl sample. Several commercial devices
are available. A substitute sample loader can be assembled
from a disposable 0.5 or 1 ml syringe fitted with a disposable
plastic tip (see Appendix).
Materials
• EcoRI- and HindIII-digested bacteriophage lambda
DNA samples containing SM Dye (other DNA samples
can be added or substituted).
• Reaction Stop Mix Dye (SM Dye): 10% glycerol, 0.5%
SDS (sodium dodecyl sulphate), 0.025% xylene cyanol
FF dye (XC), 0.025% bromphenol-blue WS dye (BPB).
This mix is added to a DNA sample after digestion to
prepare the sample for electrophoresis. The SDS helps
inactivate DNA binding proteins and releases them
from the DNA fragments and the glycerol weights the
sample so that it will layer uniformly into the slots in
the gel. The two dyes serve as visual markers of the
progress of the electrophoresis only and do not stain
DNA or proteins. The purple BPB dye will migrate with
about twice the relative mobility of the turquoise XC
dye.
• TBE electrophoresis buffer: 90 mM TRIS, 2.5 mM
Na2EDTA, 89 mM boric acid, final pH 8.2 (can be stored
as a 10x stock).
• 1% Agarose: Molten 1% agarose in TBE buffer, heated
to 100oC to melt the agarose and stored in 55oC water
bath until needed. Melt the agarose very carefully to
minimize superheating and violoent boiling.
• Ethidium bromide (EtBr): For staining gels to visualize
DNA, approximately 200 ml of 4 µg/ml ethidium
bromide in water in a shallow tray, stored covered and
protected from excessive light exposure. EtBr should
be treated as a mutagen - a compound capable of
causing genetic mutations - and bare skin should not
come in contact with the solution. It is both
photosensitive and biodegradable and dilute solutions
are often disposed of via the sink. Concentrated
solutions must be saved and disposed of as
biohazardous chemical waste.
Protocol
1. Use the molten agarose to pour a minigel as
demonstrated or according to instructions for the gel
unit in use. Illustrations for assembling a generic gel
unit are included in the Appendix. It is important to be
certain that all small agarose particles are completely
melted before use. Allow the gel to completely harden
before removing the well-forming comb. This should
take about 15 minutes.
2. Remove the comb from the solidified gel and transfer
the gel to a running unit. Submerge the gel in TBE
buffer.
3. Use a manual pipettor with a disposable plastic tip to
load 10 µl of each sample into one of the wells in the
gel. Plasmid and bacteriophage DNA samples should
be easy to load, but chromosomal DNA samples may
be quite viscous and difficult to load.
4. Once the samples have been loaded, close the unit
and apply power to the electrophoresis chamber.
Typical minigels run at 100-130 volts (60-160
milliamps), depending on the unit used. During the run,
the XC and BPB dyes will resolve into two bands, with
the BPB the faster band. Run the gel until this band is
near the end of the gel, then turn the current off and
remove the gel.
5. Transfer the gel to the staining tray containing the
ethidium bromide solution, and stain the gel for 5
minutes. Ethidium bromide is a mutagen, and gloves
should be worn or a spatula used to transfer the gel in
and out of the ethidium solution.
6. Transfer the stained gel to a destaining tray containing
water. Destain the gel for 5 minutes to remove excess
ethidium bromide.
7. The stained gel can be visualized with a UV
transilluminator or a UV mineral lamp. DO NOT LOOK
DIRECTLY AT THE UV LIGHT!! UV light causes skin
burns, is a mutagen, and will cause severe headaches
from eye damage with direct exposure. Always use a
face mask or shield.
 Introductory Experiments 73

Analysis and significance of results intensity and blurring of bands.

The results of a typical gel are shown illustrated below: d. The smearing of the EcoRI-digested lambda DNA is
caused by loading too much DNA.

During electrophoresis of DNA fragments through an

agarose gel, the fragments separate by size with smaller
fragments moving faster than larger fragments. The
relationship between size and mobility is not linear, but
can be approximated by plotting the distance migrated
versus the log(Molecular Weight).

If lambda DNA samples digested with different restriction

endonucleases are present on the same gel, note that each
different restriction enzyme produces a distinct, completely
reproducible pattern of DNA fragments. Relative separation
of individual fragments is dependent on agarose
concentration, electrophoresis conditions, and the quality
of the gel preparation.
Many different types of artefact can distort the bands
in a gel. Some of the more common gel artefacts are
illustrated below.

Using the HindIII fragments as molecular weights

standards to estimate the size of other DNA fragments.
Mobility of fragments is determined and plotted as log(Size)
versus mobility. The line drawn through the lambda DNA
fragments can be used as a standard curve for
determination of sizes of other DNA fragments present on
the same gel.

Exercise 2. Restriction endonuclease digestion of

chromosomal and plasmid DNA

Digestion of DNA with a site-specific restriction

endonuclease will generate a set of specific DNA
fragments. In this exercise, a variety of DNA samples will
be digested with the restriction enzyme EcoRI. This enzyme
recognizes and cleaves the sequence 5'-GAATTC-3'
between the G and A residues to generate the four-base
a. Gel was crooked in gel box and samples migrated off
of the gel. cohesive terminus AATT:
b. Agarose was not completely melted before gel was 5'-NNNNGAATTCNNNN-3' EcoRI 5'-NNNNG AATTCNNNN-3'
3'-NNNNCTTAAGNNNN-5' ----------> 3'-NNNNCTTAA GNNNN-5'
poured. The small specks of high concentration
agarose in the gel cause distortion in DNA bands and
bright spots in the gel. Because EcoRI recognizes and cleaves at a six-base
c. The sample well containing the EcoRI-digested lambda sequence (5'-GAATTC-3'), the number of fragments
DNA leaked at the right side, causing loss of sample generated by digestion of a DNA molecule with this enzyme
74 Tait
is determined approximately by the frequency of occurence
of the recognition site. Since there are four possible bases
that can occur at any position in DNA (A,C,G,T) the
probability of occurence of a specific base is (1/4), while
that of a specific two-base sequence is (1/4)2, a four-base
sequence (1/4)4, and a six-base sequence is (1/4)6. The
six-base EcoRI site, therefore, should occur about once
every 46 bases, or once every 4096 base pairs. EcoRI
cleaves the 2,800 base pair plasmid pUC19 only once and
will convert the circular molecule to a linear form, cleaves
the linear 50,000 base pair bacteriophage lambda DNA
five times to generate six fragments, cleaves hundreds of
times in the E. coli DNA genome, and thousands of times
in eukaryotic DNA. The larger the genome of an organism
is, the greater the number of fragments generated during
digestion with a restriction enzyme.
Several DNA samples from genomes of increasing size
will be digested with EcoRI in this exercise. If both the
enzyme digestion and the gel analysis are to be performed
in the same day, as soon as the digestion reactions have
been set up and are incubating, prepare agarose minigels
for analysis of the digested DNA samples.
Materials
• Plasmid pUC19 vector DNA: 100 µg/ml.
• Bacteriophage lambda DNA: 100 µg/ml.
• Bacterial chromosomal DNA: 100 µg/ml.
• EcoRI endonuclease: 3-5 units/µl. Keep this in ice at
all times!!
• 10x EcoRI Reaction buffer: 500 mM TRIS-HCl pH 7.0,
750 mM NaCl, 60 mM MgCl 2 , 60 mM 2-
mercaptoethanol. Most enzyme companies supply the
correct buffer with each enzyme purchased.
• Water (dH2O): Sterile, deionized or distilled.
• Manual pipet devices, 1-20 µl and 20-200 µl capability.
• Disposable conical 1.5 ml microfuge tubes and pipet
tips.
Protocol
1. For each different chromosomal DNA sample, set up
a digestion reaction in a labeled 1.5 ml conical tube
by making the following additions:
10x EcoRI buffer 5 µl
dH2O 35 µl
1 ug DNA 10 µl
Total volume 50 µl
2. Mix the contents of the tubes gently but thoroughly,
then from each tube remove 10 µl and place in a tube
labeled with the sample number and the term “-EcoRI”.
Place these 10 µl samples on ice. They are the
undigested controls and will be used to compare to
samples following digestion.
3. To the remaining 40 µl of each sample add:
EcoRI, 5-10 units 2 µl
Mix, then incubate at 37oC for 30 minutes.
4. From each digestion tube, remove 10 µl of each
sample and add to a tube labeled with the sample
name and “+EcoRI”. The remainder of each digestion
reaction should be frozen for further use.
5. You should now have two tubes containing 10 µl of
each DNA sample, one “-EcoRI” and one “+EcoRI”,
for a total of six tubes. To each of these tubes add:
SM dye 5 µl
Mix the contents of each tube, and the samples are
ready for electrophoresis. Samples can be stored on ice
or frozen for future gel electrophoresis.
Significance of procedure
This exercise has prepared reaction mixes that contain
several DNA samples of different sizes and conformations,
then digested portions of each reaction mix with the
restriction enzyme EcoRI. The samples are now ready for
analysis by agarose gel electrophoresis to determine the
effects of the restriction enzyme digestion. The same gel
electrophoresis described in Exercise 1 will be utilized.
Materials
• DNA samples prepared in Exercise 2.
• Electrophoresis materials, see Exercise 1.
Protocol
1. Prepare a 1% agarose gel in TBE buffer as in Exercise
1.
2. When the gel has solidified, assemble the gel unit.
Load 15 µl of each of the six samples. You may also
want to include one lane of the digested lambda DNA
used in the first exercise as a DNA standard.
Electrophorese as in Exercise 1.
3. Stain the gel with ethidium bromide and visualize the
DNA bands with a UV light box. A photograph of the
gel is useful, but a sketch of the gel is sufficient for
recording information.

Analysis and significance of results
A typical gel is illustrated below:
Compare each undigested (-EcoRI) with the corresponding
digested (+EcoRI) sample. Note that the migration position
of the undigested circular plasmid pUC19 DNA (a) changes
when cleaved at the unique EcoRI site to generate a linear
molecule (b). The linear undigested lambda DNA (c)
contains five EcoRI cleavage sites, and migrates as six
bands after digestion (two of the bands are of similar size
and can be difficult to resolve, but this double band will be
twice as intense as the other bands) (d). The slowly
migrating, broad, undigested bacterial chromosomal DNA
sample (e) is converted upon digestion to hundreds of
smaller, yet distinct bands (f). Note that as the size of the
genome (pUC19<lambda<E. coli) increases, the number
of cleavage sites also increases, demonstrating that larger
genomes are actually composed of larger amounts of DNA.
Exercise 3. Competent cell production
Although some bacteria naturally undergo a growth phase
when they are capable of taking up DNA, strains of E. coli,
the bacteria most commonly used in a molecular biology
lab, cannot normally take up DNA. These bacteria must
be chemically treated to be made competent for
transformation. Competent cells can be purchased from a
variety of commercial sources but can be relatively
expensive for routine classroom demonstrations and
laboratories. Cells can be made by harvesting rapidly
growing bacteria and exposing them to calcium chloride
on ice. The following protocol can be used to make
competent E. coli that are of sufficient quality for routine
use.
Materials
• 35 ml LB medium (1% Bacto Tryptone, 0.5% Bacto
Yeast Extract, 0.5% NaCl, pH 7.0-7.2) in sterile 100-
250 ml flask.
• Fresh 2 ml overnight LB culture of JM83.
• Sterile 50 or 35 ml centrifuge tube.
• Sterile 30 mM CaCl2.
Introductory Experiments 75
• Sterile 30 mM CaCl2, 15% glycerol.
• Sterile microfuge tubes.
• Ice.
• Refrigerated centrifuge. If a refrigerated centrifuge is
not available, place a clinical or counter-top centrifuge
in a refrigerator. Allowing the cells to warm up during
the centrifugation may affect the competency of the
cells.
Protocol
1. Competent cells must be made from a rapidly growing
culture of bacteria to obtain good efficiencies of
transformation. Mid-logarithmic phase of growth (3-5
x 108 cells/ml) is good for preparation of general-use
competent cells. With a fresh overnight innoculation
culture, a 1:50 dilution into a fresh culture will generally
give mid-log cells in 60-90 minutes of growth at 37oC.
If an old overnight culture is used or if insufficient
dilution is made, the bacteria will undergo a significant
lag phase before growth begins.
2. Use sterile techniques to transfer 0.7 ml of the
overnight culture of JM83 to the flask containing 35 ml
of LB. Incubate in a 37oC shaker with vigorous shaking
to allow growth. Monitor the growth of the culture every
20 minutes (A550). When absorbance is approximately
0.5, the culture is ready to harvest. This should
correspond to a mid-logarithmic phase of growth. If a
semi-log plot of A550 versus time is prepared, harvest
of cells should occur in the linear portion of the graph.
3. Although strict sterile technique is not necessary, try
to minimize contamination of the cells throughout the
following procedures. Pour the culture into a sterile
centrifuge tube. Spin 7000 rpm, 5 minutes to pellet
the cells.
4. Pour off the supernatant. Add 17.5 ml of cold 30 mM
CaCl2 (1/2 of the original culture volume). Gently
resuspend the cells.
5. Place cells on ice for 20 minutes. Cells will swell to
form spheroplasts. Cells can incubate on ice as long
as 90 minutes.
6. Centrifuge 7000 rpm, 5 minutes, at 4oC.
7. Pour off supernatant. Many strains of E. coli often form
a halo instead of a normal pellet.
76 Tait
8. Add 3.5 ml of cold 30 mM CaCl2, 15% glycerol.
GENTLY RESUSPEND THE CELLS. If resuspension
is too harsh, competency may decrease. Return cell
suspension to ice.
9. Label 17 sterile microcentrifuge tubes “cJM83”. Aliquot
200 µl of competent cells into each tube. Cap tubes.
Cells can be used immediately or stored in a freezer
for future use. To freeze, move the tubes to a pre-
chilled rack in the freezer for storage. Cells can be
stored at -20oC (normal lab freezer) for several weeks
or at -70 oC for months without significant loss of
competency. Recombination deficient strains (recA-
strains, in particular) rapidly lose viability/competency
when stored in a freezer.
10. If competent cells are made and stored for use in a
lab exercise, it is wise to transform one tube with a
pure plasmid DNA sample prior to use to verify that
the cells have not lost competency during storage.
Larger numbers of competent cells can be prepared
by scaling all procedures up as needed. When culture
volumes are increased, be certain that the culture has
a large surface area to maintain adequate aeration in
the growing culture.
Exercise 4. Transformation of competent cells with
pUC19 and pUC19 recombinants
DNA molecules can be inserted into bacteria by first
chemically treating the bacteria to make them competent,
or able to take up DNA. This chemical treatment is often
accomplished by exposing the bacteria to specific salts
that cause the bacteria to swell and become capable of
binding DNA. Treatment of E. coli with CaCl 2 gives
reproducible transformation results, although higher levels
of competency can be attained with other procedures. After
exposing the competent cells to DNA on ice, a 43oC heat
shock is required to make the competent cells take up the
bound DNA.
In this exercise, E. coli strain JM83 will be transformed
with the plasmid pUC19. This plasmid contains genes that
allow its own replication in the bacterium and contains a
gene (bla) that encodes ß-lactamase, an enzyme that
confers resistance to ampicillin. The host strain JM83 is
sensitive to and will not grow in the presence of ampicillin,
while JM83 containing pUC19, indicated by JM83(pUC19),
will grow and form colonies in the presence of the antibiotic.
This plasmid also contains a genetically engineered portion
of the lac operon of E. coli. When exposed to the inducing
compound IPTG, cells containing pUC19 synthesize the
enzyme ß-galactosidase. This activity can convert the
colorless compound X-gal to a blue compound during the
growth of the cells. When the strain JM83(pUC19) is plated
on medium containing ampicillin, IPTG and X-gal, the
resulting colonies will be dark blue in color.
The plasmid pUC19 was designed with a series of
unique restriction cleavage sites within the coding region
of the ß-galactosidase gene. This region, designated the
multiple cloning site or MCS, is used for the specific
insertion or cloning of extra DNA fragments. When a
fragment is inserted, the β-galactosidase gene is
interrupted and the enzyme can no longer be synthesized.
Thus, a strain containing pUC19 with an extra DNA insert,
designated JM83(pUC19:insert), will still form colonies in
the presence of ampicillin, but in the presence of IPTG
and X-gal the colonies will remain white rather than blue.
Thus, bacteria containing the wild-type pUC19 vector can
be distinguished from cells containing a recombinant
pUC19 plasmid with an extra DNA insert.
To transform cells with pUC19, the competent cells
will be placed at 43oC, then directly plated on nutrient plates
containing 100 ug ampicillin/ml as a selective antibiotic.
Incubation of the plates at 37oC will allow colonies to form.
The presence of the compounds IPTG and X-gal will be
used to distinguish the original vector from recombinant
derivatives containing DNA inserts. The wild-type vector
will cause the formation of blue colonies and recombinant
derivatives present in the pUC19:E. coli DNA library will
cause the formation of white colonies.
Flow chart, Exercise 4
Materials
• Plasmid pUC19 vector DNA: 100 µg/ml.
• pUC19:E. coli library DNA: 100 µg/ml.
• Competent E. coli cells: CaCl2 treated competent JM83
cells, 100 µl aliquots, stored -20oC.
• Sterile dH2O.
• LB agar plates containing ampicillin for selection of
pUC19 transformants: 1% Bacto Tryptone, 0.5% Bacto
Yeast Extract, 0.5% NaCl, 1.5% Bacto agar, pH 7.0-
7.2. Autoclave to sterilize, cool to 50oC, add ampicillin
to 100 µg/ml, pour petri plates, and cool. Other
complete E. coli nutrient media can be substituted, as
long as ampicillin is present. Do not use minimal media,
as most laboratory strains of bacteria have several
nutritional deficiencies that require specific
supplements that are generally present in rich media.

• 10 mM IPTG: 23.8 mg IPTG (isopropyl-β-D-
thiogalactopyranoside)/ml dH2O.
• 5% X-gal: 50 mg X-Gal (5-bromo-4-chloro-3-indolyl-
β-D- galactopyranoside)/ml dimethylformamide.
• 43oC temperature block or water bath.
• 37oC incubator.
Protocol
1. Prepare six LB-Ap plates for transformation by adding
IPTG and X-gal to each plate. To a sterile tube add 60
µl 10 mM IPTG and 300 µl 5% X-gal. Mix solution.
Place 60 µl of this IPTG/X-gal mix on the surface of
an LB-Ap plate. Dip a glass spreader in 95% ethanol
and flame to sterilize. Use the spreader to distribute
the IPTG/X-gal mix evenly over the surface of the plate.
Replace the lid on the plate and invert the plate. Repeat
this process for each of the remaining 5 plates. If you
attempt do do all of the plates at the same time, the
solution may soak into the center of the plates and will
not be uniformly distributed over the surface. Allow
the solution to soak into the surface of the plates for
15-30 minutes (if possible, place the plates in a 37oC
incubator during this time period).
2. Thaw three tubes of competent cells at room
temperature. As soon as cells are thawed, label one
tube “-DNA”, one tube “+pUC19”, and one tube
“+library” and place all tubes on ice.
3. To the “-DNA” tube add 10 µl sterile ddH 2O, to the
“+pUC19” tube add 10 µl (1 µg) of pUC19 DNA, and
to the “+library” tube add 10 µl of pUC19:EC library
DNA. Place tubes on ice for at least 15 minutes (length
of time is not crucial here). This allows DNA to bind to
the competent cells. While tubes are on ice, adjust a
water bath to 42-43oC.
4. Heat pulse the cells to cause DNA uptake. Transfer all
three of the tubes of competent cells containing DNA
to the 42oC bath for 90 seconds, then transfer to a
room temperature rack.
5. Add 10 µl of one of the transformed cell samples to an
LB-Ap-IPTG-Xgal plate and the rest (100 µl) to another
plate. Dip the glass spreader in ethanol, flame, and
use to distribute the cells evenly over the surface of
each plate. Invert the plates and label with amount of
cells and type of DNA (such as 10 µl, pUC19). Repeat
for each of the tubes of transformed cells (you should
end up with no tubes of transformed cells left over
and have six labeled plates with cells spread on them).
Place plates in a 37oC incubator for 12-18 hours to
allow colonies to form and color to develop. Plates
can be stored in a refrigerator and color will continue
to develop.
Analysis and significance of results
After the plates have been allowed to incubate and colonies
have formed and colored, compare all the plates. The
following results are typical:
• JM83 transformed with no DNA should give no distinct
colonies but may have some smearing or poor growth
in areas of dense numbers of cells.
• JM83 transformed with pUC19 DNA should give many
distinct colonies, nearly all of which (>99%) should be
blue. The occasional white colony will be a contaminant
or a mutant derivative of pUC19 in which the ß-
galactosidase gene is no longer active. By counting
Introductory Experiments 77
the number of colonies on a plate and dividing by the
amount of transforming DNA represented on the plate,
it possible to calculate the efficiency of transformation
in terms of transformants/µg DNA. Example: 1 µg of
pUC19 DNA was added to 100 µl of competent cells,
and 1 µl of this mix was plated on an LB-Ap plate,
resulting in 227 colonies. The amount of DNA
represented on the plate is 10 µl/110 µl x 1 µg = 0.1
µg. Transformation efficiency is 227 colonies/0.1 µg,
or 2.27 x 103 transformants/µg DNA.
• JM83 transformed with pUC19:E. coli library should
give similar numbers of colonies when compared with
the pUC19 transformation, but only a percentage of
the colonies will be blue. The blue colonies are the
result of transformation with pUC19 containing no
additional DNA insert, and the white colonies are
caused by transformation with recombinant pUC19
plasmids. The transformation efficiency can be
calculated for the DNA as described above and the
percentage of recombinant molecules can be
determined by the calculation:
100 x # white colonies/# total colonies.
This exercise demonstrates two fundamental principles of
recombinant DNA methods:
1. DNA can be inserted into bacteria to change the
properties of the cells (ampicillin-sensitive cells
converted to ampicillin-resistant colonies).
2. DNA fragments can be re-arranged to change the
genetic properties of the DNA molecules (blue colonies
caused by pUC19 are converted to white colonies
when DNA fragments are inserted into pUC19 DNA).
These principles can be further examined by isolation and
examination of plasmid DNA present in the transformant
colonies.
Exercise 5. Transformation of competent cells with
pUC19 and pBR322 plasmid DNA
One of the most important concepts of DNA biology is that
genes are composed of DNA and that the introduction of
DNA into a cell can change the physical properties of the
cell. This can be illustrated with petri plates containing a
simple nutrient medium (Luria broth, Tryptone, Nutrient
agar, essentially any medium that will allow the growth of
E. coli), a small amount of plasmid DNA, and competent
E. coli bacterial cells.
This exercise uses E. coli JM83 cells that have been
made competent, or able to take up DNA. The cells were
grown to mid-logarithmic phase, then harvested and
resuspended in 30 mM CaCl2. After incubation on ice for
30 minutes, the cells were again harvested and
resuspended in 30 mM CaCl2 with 15% glycerol. Cells were
dispensed into 0.2 ml volumes in sterile 0.5 ml tubes. Each
of these tubes contains sufficient cells for at least 4 different
transformation reactions. Competent cells may slowly lose
their ability to take up DNA if not stored at -70oC. For this
reason, the competent cells are shipped in dry ice to arrive
the week before the exercise and are stored in a freezer at
about -5oC until used.
A DNA sample containing two types of pure plasmid
DNA, pUC19 and pBR322, at a concentration of 100 µg/
ml will be used to demonstrate that DNA can change cellular
78 Tait
properties. The plasmid pUC19, a common plasmid cloning
vector used to carry and propagate other DNA fragments
in bacteria, has two genes of interest: one confers
resistance to the antibiotic ampicillin, and the other encodes
a ß-galactosidase gene derivative that produces a protein
that can help the bacteria metabolize derivatives of the
sugar galactose. When the colorless compound X-gal is
added to the growth medium, the ß-galactosidase protein
can metabolize the X-gal into a colored derivative that turns
the bacterial colonies blue.
The second plasmid DNA provided is pBR322, one of
the older plasmid cloning vectors. Like pUC19, this plasmid
confers resistance to ampicillin, but it also confers
resistance to the protein synthesis inhibitor tetracycline.
Just like bacteria containing pUC19, bacteria containing
pBR322 will be able to grow in medium containing
ampicillin. Since pBR322 does not contain the ß-
galactosidase gene derivative, cells containing this plasmid
will be unable to metabolize X-gal to a colored compound
and will remain white when exposed to X-gal. Bacteria
containing pBR322 will, however, be able to grow in the
presence of a concentration of tetracycline that kills cells
containing pUC19.
The bacterial strain JM83 is sensitive to ampicillin and
will not grow on nutrient plates in the presence of the
antibiotic at a concentration of 100 µg/ml. When either
pUC19 or pBR322 is inserted into the competent JM83
cells, the cells become transformed and are able to grow
in the presence of the antibiotic. These two plasmids can
thus cause the same change in bacterial phenotype - ability
to grow in the presence of ampicillin - and this property
cannot be used to distinguish between cells containing one
of these two plasmids.
Genetic maps of the plasmids pUC19 and pBR322
However, if the compounds X-gal and IPTG are also
added to the ampicillin plate, the ß-galactosidase gene
present on pUC19 will cause bacteria containing this
plasmid to form blue colonies, while bacteria containing
pBR322 will form white colonies. The difference in
phenotype associated with these plasmids - ability of cells
containing pUC19 to form a blue colony - allows rapid
sorting of colonies formed by cells containing each of the
two types of plasmid. This demonstrates that two plasmids
that confer the same phenotypic property (such as ability
to grow in the presence of ampicillin) can be readily
distiguished if the plasmids differ in ability to confer a
second phenotype (such as ability to metabolize X-gal to
a blue compound).
This exercise will also demonstrate a second important
principle of DNA manipulation: when two genes are both
present on the same DNA fragment, selection for one of
the genes will force maintenance of the second gene as
well. As the transformed bacteria grow and form colonies
in the presence of ampicillin but in the absence of
tetracycline, there is no selective pressure that requires
the expression of the tetracycline resistance gene present
on pBR322. Nevertheless, because the tetracycline
resistance gene is part of pBR322, growth in the presence
of ampicillin forces the maintenance of pBR322 and also
selects for the covalently attached tetracycline resistance
gene. If the blue and white colonies obtained on the
ampicillin plate containing X-gal and IPTG are transferred
to a nutrient plate containing tetracycline at a concentration
of 20 µg/ml, the blue colonies containing pUC19 will be
unable to grow and the white colonies containing pBR322
will be able to form colonies. This is the fundamental
principle that allows a plasmid or a viral DNA molecule to
be used as a vector to carry and propagate exogenous, or
extra, DNA fragments. DNA fragments that are covalently
inserted into a vector by the use of restriction enzymes
and DNA ligase will be maintained as the carrier vector
molecule replicates in a host cell.
Materials
• Three nutrient agar plates containing 100 µg/ml
ampicillin (NA+Ap plates).
• One nutrient agar plates containing 20 µg/ml
tetracycline (NA+Tc plates).
• A water bath or temperature block at 43oC.
• Incubator for plate culture (this can be performed at
room temperature, but growth of colonies will take two
days).
• Glass spreader bar.
• Ethanol or isopropanol for sterilizing glass spreader
bar.
• One 0.2 ml tube of competent JM83 (store these in a
normal freezer [not frost-free if possible] until needed,
then on ice).
• Ten µl of pUC19/pBR322 mixed plasmid DNA at 100
µg/ml.
• 2% X-gal in dimethylformamide (this solvent is
necessary for X-gal).
• 100 mM IPTG in sterile water.
• Sterile toothpicks.
Procedure
1. Since X-gal and IPTG are not usually added to nutrient
plates when the plates are liquid, it will be necessary
to add these compounds to the surface of the solid
plates prior to use. Place 0.1 ml of the X-gal in a 1.5
ml microcentrifuge tube (not a polystyrene tube - the
X-gal solvent may melt the plastic). Add 20 µl of IPTG
to the tube and mix the two solutions to make an X-
gal/IPTG mixture.

2. Place 60 µl of the X-gal/IPTG mixture on the surface
of each of two of the plates containing ampicillin
(NA+Ap). Save one NA+Ap plate and the NA+Tc plate
for later use. Dip a glass spreader in alcohol and then
ignite the alcohol in a burner flame to sterilize the
spreader. Cool the spreader by touching the agar
surface, then spread the X-gal/IPTG evenly across the
surface of one of the NA+Ap plates. Again sterilize
the spreader and spread the X-gal/IPTG mixture on
the second NA+Ap plate. Invert the plates and label
“+Xgal/IPTG”. This step allows the coloring agents to
soak into the surface of the agar. The agar surface
may cloud as the dimethylformamide solvent dissipates
and the X-gal precipitates. It is important to add the X-
gal/IPTG mixture shortly before the plates are used
because the X-gal can break down and may not color
well if too old.
3. Place a tube of competent cells on ice and allow to
thaw. Add the 10 µl of mixed plasmid DNA into the
thawed cells and gently mix in. Return the cells to the
ice.
4. Allow the tube to stand in the ice bucket for 15 to 20
minutes to allow the DNA to stick to the surface of the
competent cells.
5. To make the DNA enter the cells, place the tube in a
43oC water bath (be careful with the temperature, too
hot or too cool will not work as well). Allow the tube to
incubate at 43oC for 60 seconds, then remove from
the water bath and place at room temperature.
6. The transformation is complete. It is now necessary
to plate the transformation mix on selective plates to
detect the transformants and inhibit the growth of the
non-transformed cells. Transfer 20 µl of the
transformed cells to one nutrient plate containing
ampicillin, IPTG, and X-gal. Use a sterile spreader to
distribute the cells. Label the plate “20 µl”. Spread the
remainder of the transformed cells on the second plate
and distribute uniformly with a sterile spreader. Label
the plate “180 µl”.
7. Incubate the plates overnight at 37oC to allow growth
of colonies. Check the plates for colonies after 18 hours
growth and transfer the plates to a refrigerator for
storage if the colonies are sufficiently large (the size
of a typewritten”o”) or are extremely numerous (>300
per plate). Although the colonies will stop increasing
in size, blue color will continue to develop in the cold.
If allowed to remain at 37oC too long, non-transformed,
ampicillin-sensitive “feeder” colonies will begin to form
as the ampicillin-resistant colonies degrade the
ampicillin in the medium.
8. If the transformation has been successful, both blue
and white colonies should be present on the surface
of the two plates. The blue colonies are formed as a
result of the transformation of bacteria with pUC19 and
the white colonies are formed as a result of the
transformation of bacteria with pBR322. This can be
verified by using the ability of pBR322 to allow growth
in the presence of tetracycline. To check transformants
for this phenotypic property, label the back of the
remaining NA+Ap plate and the NA+Tc plate with the
numbers “1” to “40” and your initials as indicated
below:
Introductory Experiments 79
9. Touch a sterile toothpick to a blue colony on one of
the NA+Ap X-gal/IPTG plates and make a short streak
of cells over the number “1” on the NA+Ap plate and
the NA+Tc plate. Repeat this for an additional 19 blue
colonies and for 20 white colonies. Incubate both plates
overnight at 37oC to allow the growth of the bacteria.
Analysis and significance of results
Since both the blue and the white colonies were originally
obtained following growth on an NA+Ap X-gal/IPTG plate,
all of these colonies should again grow on the NA+Ap plate
but, since X-gal and IPTG are no longer present, all colonies
should remain white. Only the white colonies obtained from
the NA+Ap X-gal/IPTG plate should form colonies on the
NA+Tc plate, confirming that the transformants that
originally formed white colonies on NA+Ap X-gal/IPTG
contained pBR322. Note that although the original selection
for transformed bacteria involved resistance to ampicillin,
resistance to tetracycline was also maintained by nearly
all of the ampicillin-resistant white colonies. Since the genes
conferring resistance to ampicillin and tetracycline are both
present on the same DNA molecule (the plasmid pBR322),
selection for one of the two genes (ampicillin resistance)
also selects for the presence of the non-selected gene
(tetracycline resistance).
It is possible to obtain ampicillin-resistant white
colonies that cannot grow on tetracycline and ampicillin-
resistant blue colonies that can grow on tetracycline. When
the DNA from the plasmids present in these colonies is
isolated and examined by digestion with restriction
enzymes, the first type of colony can often be demonstrated
to be caused by the occurrence of a deletion that removes
part or all of the ß-galactosidase gene of pUC19, causing
inability to metabolize X-gal to a blue compound, or a
deletion that removes part of the tetracycline resistance
gene, causing loss of tetracycline resistance. These
deletions occur naturally in bacteria as an aspect of normal
DNA replication, recombination, and repair processes.
The second type of colony is most commonly caused
by the presence of bacteria containing both pUC19 and
pBR322 in the same colony. This can be verified by
streaking the bacteria out on an NA+Ap X-gal/IPTG plate
and incubating to obtain isolated colonies that are either
blue and tetracycline-sensitive or white and tetracycline-
resistant. While both plasmids can occassionally be
inserted into the same bacterial cell during the
transformation process, pUC19 and pBR322 replicate by
very similar mechanisms and are said to be incompatible
80 Tait
with one another. When incompatible plasmids are inserted
into the same bacterium and the cell is grown in the
absence of selective pressure designed to force
maintenance of both plasmid types, the plasmids will
segregate during division of the transformed bacterium and
the resulting progeny will contain one or the other of the
two plasmids.
Exercise 6. Comparison of plasmid and bacteriophage
cloning vectors
Much of the scientific utility of recombinant DNA technology
is based on the use of self-replicating DNA elements to
serve as carriers for DNA fragments that are not capable
of replication in bacteria. Bacterial cloning vectors are
based on either bacterial plasmids or bacteriophage.
Plasmids are naturally occurring, circular DNA molecules
that can replicate as mini-chromosomes in bacteria. When
isolated from nature, these DNA molecules also generally
encode resistance to one or more antibiotics and may
contain genes that allow transfer of the plasmid DNA from
one cell to another during bacterial mating. Most cloning
vectors derived from plasmids retain the plasmid origin of
DNA replication and one or more antibiotic resistance
genes, such as the ß-lactamase gene, which allows
sensitive bacteria to form colonies on solid medium
containing ampicillin. With plasmid cloning vectors,
selection of bacteria containing the vector requires selection
for a phenotype, or physical characteristic, associated with
a gene present on the vector DNA molecule.
Cloning vectors have also been constructed from
bacteriophage, viruses that replicate in bacteria. Two types
of bacteriophage cloning vectors, derived from either the
double-stranded, linear DNA bacteriophage lambda or the
malespecific, single-stranded, circular DNA bacteriophage
M13, are in common use in E. coli. Detection of cells
containing either of these types of vector does not require
selection for a phenotypic marker, but is based on the ability
of the bacteriophage to form a plaque in a lawn of host
bacteria, a property associated with the replication of the
viral DNA vectors.
Lambda has a large genome (approx. 50 kilobase pairs
of double-stranded DNA) that can, on insertion into a
bacterial host, activate either of two sets of viral genes.
One set of genes allows the bacteriophage to undergo a
lytic cycle during which progeny phage are produced and
the infected bacterial cell bursts open, releasing the
daughter phage into the medium. When activated, the other
set of genes causes the bacteriophage DNA to lysogenize,
or insert itself into a specific location in the bacterial
genomic DNA, where it remains silent while the bacterial
cell undergoes normal cellular functions. Certain conditions,
such as DNA damage, will induce the lysogen, activating
the lytic genes. The bacteriophage DNA then excises from
the host chromosome, produces progeny, and lyses the
host cell. When bacteria are grown on the surface of solid
medium from a low density to a uniform lawn of cells, the
presence of lambda can be detected by the appearance
of plaques, circular clear zones in the cloudy lawn of host
bacteria. As the host bacteria grow to form the indicator
lawn, successive cycles of infection/production of progeny/
cell lysis cause the death and lysis of all of bacteria in a
circular zone surrounding even a single lambda
bacteriophage. Cells that are able to lysogenize the lambda
DNA into their own genome become resistant to infection
and may form small colonies within the zone of lysis. The
ability of lambda DNA to cause the lysis of bacteria serves
as the selective marker for the presence of cloning vectors
derived from this bacteriophage. In marked contrast to
plasmid cloning vectors, which require phenotypic selection
to detect cells containing the vector, the replication of a
lambda cloning vector provides a plaque, the immediate
means of detection of cells containing the vector. Because
the lambda plaque is basically a zone of lysed cells,
however, the plaque indicates only where the infected cells
were. Lambda vectors and recombinants derived from them
must generally be maintained not as viable bacterial strains,
but as stocks of virus particles.
An M13 bacteriophage particle contains a single-
stranded, circular DNA genome of about 8 kilobase pairs.
These particles will only infect host bacteria that are
producing the F-pilus protein, which is part of the mating
apparatus encoded by the large F plasmid. Bacteria that
are male, or F+, can be infected by the M13 phage particle.
The entering single-stranded viral DNA is converted to and
replicates as a double-stranded circular DNA. Single-
stranded progeny phage identical to the original infecting
DNA are produced, coated with viral coat proteins, and
extruded through the bacteria cell wall into the medium
without lysing the host cell. When propagated in a sensitive
host grown on the surface of a solid medium, cloning
vectors derived from M13 will form small, circular zones of
infected cells that are extruding phage particles. In contrast
to plaques formed by lambda vectors, these plaques are
cloudy rather than clear and contain viable, infected cells
that can be propagated as bacterial strains. While these
plaques are biologically quite different than those induced
by strains of lambda, the plaques appear similar to those
induced by lambda. M13 vectors and recombinants derived
from them can be maintained as either viable infected
bacteria containing the double-stranded circular replicating
form of virus DNA or as stocks of viral particles containing
single-stranded circular DNA.
This exercise will use JM101, an F+ strain of E. coli
that will allow growth of plasmids and M13 to illustrate the
similarities and differences in the use of these different
types of cloning vector.
Materials
• Six tubes competent JM101 bacteria.
• 11 µl pUC19 DNA, 100 µg/ml (Ampr plasmid vector).
• 11 µl mp19 DNA, 100 µg/ml (M13 cloning vector).
• Two LB plates containing 100 µg/ml ampicillin (LB-
Ap).
• Two LB plates (LB).
• Twenty-five ml LB-soft agar (LB containing 0.8% agar).
• Sterile 5-10 ml glass or plastic tubes.
Procedure
1. Place the tubes of competent cells in an ice bucket to
thaw. Label the two LB-Ap plates “pUC19 1 µl” and
“pUC19 10 µl”. Label two LB plates “mp19 1 µl” and
“mp19 10 µl”. Leave the plates at room temperature
to warm up for about 10 minutes.
2. When the competent cells have thawed, label the tubes
as below:

Tube 1 pUC19 1 µl
Tube 2 pUC19 10 µl
Tube 3 mp19 1 µl
Tube 4 mp19 10 µl
3. Add the appropriate amount of each of the DNA
samples to the labeled tubes of competent cells and
gently mix in. Allow to incubate on ice for 20 minutes.
4. Label four of the capped sterile glass or plastic tubes
as below:
Tube 1 pUC19 1 µl
Tube 2 pUC19 10 µl
Tube 3 mp19 1 µl
Tube 4 mp19 10 µl
5. Use a microwave or boiling water bath to melt the 25
ml of LB-soft agar. Place the melted soft agar in a 55oC
bath for at least 5 minutes to allow the temperature to
decrease from boiling. Use a sterile pipet to dispense
3 ml of the liquid agar into the tube labeled “Tube 1
pUC19 1 µl”. Immediately use a pipet device and sterile
tip to transfer the competent cell/DNA mixture in the
tube labeled “pUC19 1 µl” into the 3 ml of liquid agar .
Pour the mixture onto the surface of the LB-Ap plate
labeled “pUC19 1 µl” and gently rotate the plate to
distribute evenly over the surface of the plate. Carefully
place the overlaid plate aside to solidify and do not
move it for 5 minutes. If this process is too slow, the
agar will solidify in the tube or in lumps on the surface
of the plate. If the overlaid plate is inverted too soon
after the pouring process, the soft agar will slide off of
the agar plate.
6. Repeat this overlay for each of the remaining tubes of
competent cells.
7. Incubate the plates at 37oC to allow growth of the
bacteria.
Analysis of results
Following 12-18 hours of incubation at 37oC, the bacteria
will have grown sufficiently to compare the difference in
the two types of vectors. For the cells transformed with
pUC19, the ampicillin in the LB plate rapidly diffuses into
the soft agar overlay and retards the growth of the non-
transformed cells. Cells that contain the plasmid are
resistant to the antibiotic and form small colonies in and
on the surface of the soft agar overlay.
For each of the bacteriophage vector transformations,
the non-transformed bacteria will have formed a fairly
uniform layer of cells called a lawn. The M13 mp19 vector
will cause numerous holes and depressions in the lawn.
These are best viewed by holding the plate up to a bright
light.
Note that as the size of the vector increases, the
number of transformants decreases (# pUC># mp19). This
is principally caused by the difference in the sizes of these
vectors (about 3 kb and 8 kb).
Exercise 7. The miniscreen: Rapid isolation of plasmid
DNA
The construction of a library of recombinant plasmids
involves the digestion of chromosomal and vector DNA
with a restriction enzyme, followed by joining chromosomal
Introductory Experiments 81
DNA fragments to the linearized vector DNA with the
enzyme T4 DNA ligase, followed by insertion of the DNA
into a host cell. Because the presence of restriction
enzymes can interfere with the ligation process, the
digested DNA samples are generally extracted with phenol/
chloroform to remove protein. Then, because ligation
activity is not optimal in the buffer used for restriction of
the DNA’s, samples are precipitated with ethanol, washed
with 70% ethanol to remove salts, dried, and resuspended
in ligation buffer. The enzyme T4 DNA ligase, which uses
ATP as a co-factor, is added to seal the nicks in the DNA
molecules and generate recombinant molecules. The
ligated DNA sample can then be used to transform
competent cells to give blue and white colonies.
The blue and white colonies obtained after
transformation of cells with a ligated DNA sample can be
cultured and the plasmid DNA present in the cells extracted
and examined. When purifying circular plasmid DNA from
a bacterial cell, it is necessary to separate the plasmid
away from the chromosomal DNA. Differences in the
physical properties of these two types of DNA facilitate this
separation. While purification of large (milligram) amounts
of plasmid can be somewhat time-consuming and involve
the use of large cultures (typically 1 liter) of bacteria, a
variety of rapid isolation procedures allow the purification
of a small amount of plasmid DNA (1- 5 µg) from a small
culture (1-10 ml). The DNA obtained by these small-volume,
rapid-isolation methods, generally referred to as
“miniscreens” or “minipreps”, is not as pure as that
obtained by more elaborate methods, but is suitable for
many characterization and cloning procedures.
These miniscreen procedures arose from the need to
quickly sort through a number of bacterial transformants
that contained recombinant DNA molecules of potential
interest. A typical gene isolation experiment might generate
20 candidates for the desired gene construction. The time,
expense and labor involved in purifying the DNA from a 1
liter culture of each candidate were found to be quite
annoying, and abbreviated protocols were developed to
allow the simultaneous screening of many candidates.
Rapid miniscreen procedures take advantage of the
different purification properties of chromosomal DNA and
supercoiled plasmid DNA to obtain a partial purification of
the plasmid from a small culture. Steps of the process are
generally performed in 1.5 ml plastic tubes, and
centrifugation is in a microcentrifuge that can spin 12-24
tubes at 12,000 to 16,000x gravity. Spins used to remove
precipitates are on the order of 5-15 minutes, and the entire
miniscreen process will take about 90 minutes to purify
the plasmid DNA from 12 samples. These protocols
facilitate both the mass screening of transformants
containing DNA molecules of potential interest and the rapid
analysis and manipulation of DNA samples of particular
interest.
Following transformation of JM83 with the pUC19:E.
coli library DNA, incubation of the LB-Ap plates for 12-18
hr should result in the formation of bacterial colonies on
the surface of the plates. Those transformants that contain
only pUC19 are both Apr and able to metabolize X-gal to a
blue compound and form blue colonies, while those cells
that contain pUC19 plasmids with DNA inserts are Apr but
unable to metabolize X-gal and therefore form white
colonies. The ratio of white to blue colonies is an indicator
of the frequency of recombinant transformants in the
population.
82 Tait

To characterize the plasmids in the recombinant RNase stock. Invert to mix. Incubate 10 min at 37oC.
transformants, white colonies are picked with a sterile loop 8. Add an equal volume (approx. 700 µl, simply fill the
and transferred into 2 ml cultures of LB medium, allowed remainder of the space in the tube) of isopropanol.
to grow for 6-18 hr at 37oC with shaking, then subjected to Invert tubes several times to mix. Immediately
a miniscreen procedure. These cultures can either be centrifuge 5 min at room temp in a microcentrifuge.
inoculated the day before needed or grown several days Pour off and discard supernatants.
in advance and stored in a refrigerator until needed. Long 9. Wash DNA pellets by adding 1 ml of 70% ethanol to
term storage of cells for DNA extraction is best each tube. Invert several times to mix. Centrifuge 3
accomplished by harvesting the cells from the cultures (step min at room temp. Pour off ethanol and use a Kimwipe
1 below), adding the SET buffer, and freezing the cell to dry the lip of each tube. Vacuum dry the DNA pellets.
pellets. To proceed with the miniscreen, thaw the pellets Resuspend each pellet in 20 µl dH2O. After DNA has
and vortex to resuspend the cells, then resume with step been allowed to resuspend for 10 minutes on ice, tap
3. the tubes gently to help resuspend the DNA, then
centrifuge 20 seconds to collect solution in the bottom
Materials of the tubes. The DNA is now ready to be digested
• LB medium: 1% Bacto Tryptone, 0.5% Bacto Yeast with restriction enzymes or can be stored frozen until
Extract, 0.5% NaCl, pH 7.0-7.2 (sterilized) for further use.
propagation of cultures to be miniscreened. Any
complete nutrient medium can be substituted. Flow chart, Exercises 7 and 8
• One 2 ml LB E. coli JM83 culture, grown at 37oC with
shaking for 8-15 hours.
• One 2 ml LB E. coli JM83 culture containing the
plasmid pUC19, grown at 37oC with shaking for 8-15
hours.
• Four 2 ml LB E. coli JM83 cultures from white
recombinant colonies obtained from the pUC19:E. coli
library, grown at 37oC with shaking for 8-15 hours.
• SET buffer: 20% sucrose, 50 mM TRIS-HCl pH 7.6,
50 mM EDTA.
• Lytic mix: 1% SDS, 0.2 N NaOH.
• Sodium (Na) acetate: 3.0 M, pH 4.8. Make 3 M acetic
acid and 3 M Na acetate, then mix to pH 4.8. If not
made this way, miniscreens will not necessarily work
well. Store at 4oC.
• RNase stock: Pancreatic ribonuclease A (RNase A), 1
mg/ml in 0.1 M sodium acetate, 0.3 mM EDTA.
• Isopropanol: Room temp.
• Ethanol: 70%, room temp. (70% isopropanol can be
substituted).
• Water (dH2O): Sterile, deionized or distilled.
• Ice.
• Conical microcentrifuge tubes and pipet tips.

Protocol
1. Transfer 1.5 ml of each culture to a labeled
microcentrifuge tube. You should have a total of six
tubes. Spin 1 min to pellet cells. Pour off and discard
supernatants.
2. Resuspend cell pellets in 150 µl of SET buffer. Vortex
or agitate to resuspend cells.
3. To each tube add 350 µl of Lytic mix. Invert several
times to mix. Cells will lyse and solution will clear
slightly. Viscosity increases.
4. Place in ice bath and chill approx. 10 min. Solution
will begin to cloud as SDS precipitates.
5. To each tube, add 250 µl of cold Na acetate buffer. Exercise 8. Characterization of pUC19 recombinant
Invert to mix. Return tubes to ice bath and incubate DNAs
15 min. SDS and chromosomal DNA will precipitate
during this incubation. The miniscreen DNAs will now be digested with restriction
6. Centrifuge tubes 10 min at 4oC in a microcentrifuge. endonuclease EcoRI, the same enzyme that was used to
Pour supernatants (approx. 700 µl) into clean, labeled construct the library. Any DNA fragments that were inserted
microcentrifuge tubes. Discard tubes containing the in the unique EcoRI site of pUC19 will be released upon
pellets. digestion, and agarose gel electrophoresis will allow
7. To each tube containing a supernatant, add 2 µl of characterization of the size and number of additional
fragments.
 Introductory Experiments 83

Materials Lane a. HindIII lambda DNA

• Miniscreen DNAs. Lane b. JM83 (no plasmid)
• Ice. Lane c. JM83 (pUC19)
• Conical microcentrifuge tubes and pipet tips. Lane d. JM83 (recombinant #1)
• Endonuclease digestion materials, see Exercise 2. Lane e. JM83 (recombinant #2)
• Gel electrophoresis materials, see Exercise 1. Lane f. JM83 (recombinant #3)
Lane g. JM83 (recombinant #4)
Protocol
1. If you plan to digest more than a few samples, it is Note that no specific DNA fragments other than a faint
convenient to make a mix containing 10x EcoRI buffer, background of chromosomal DNA fragments are observed
H2O, and EcoRI enzyme, aliquot this mix into reaction in the miniscreen DNA prepared from the JM83 culture
tubes, then to each tube add a separate DNA sample. containing no plasmid, while the five samples prepared
For example, for each six miniscreens to digest, plan from Apr transformants all contain specific DNA bands. This
on a 20 µl reaction for each digest, with 2 µl of further demonstrates that the presence of the plasmid DNA
miniscreen DNA diluted into 18 µl of reaction mix. in the transformants is associated with the conversion to
Prepare the following mix: ampicillin resistance. In addition, the presence of inserted
DNA fragments correlates with the inability of recombinant
10x EcoRI buffer 12 µl pUC19 plasmids to generate blue transformant colonies.
dH2O 96 µl Different recombinant colonies may contain inserts of
EcoRI enzyme, 20 units 2-5 µl different sizes. Small inserts may not be detected by
Total volume 110-113 µl agarose gel electrophoresis.

Label six tubes for the digestion reactions, and Many of the gel artefacts commonly associated with
dispense 18 ul of this mix into each tube. Then add 2 miniscreen DNA are illustrated below:
µl of a miniscreen DNA to each of the tubes, for a total
of six different reactions. This is more convenient than
setting up six individual reactions.
2. Incubate at 37oC for 30-60 min, then remove 8 µl from
each digestion and place on a Parafilm strip. Add 3 µl
of SM dye to each sample.
3. Subject samples to electrophoresis on a 1% agarose
gel in TBE buffer. Run a sample of EcoRI- or HindIII-
digested lambda DNA as a molecular weight standard.
4. Following electrophoresis, staining and visualization
of the DNA fragments will reveal any additional
fragments present in the pUC19 recombinants. While
a photographic record of the gel allows convenient
measurement of fragment position for the purpose of
calculating mobilities, and hence determining
molecular weights, photos are expensive. A ruler can
be laid next to the gel on the UV box, and a drawing Lane a. Undigested DNA with both supercoiled (dark
with measurements added used to construct a graph bands) and open circular (stippled bands) forms.
of fragment mobilities. Lane b. Partially digested plasmid DNA sample with insert
(bottom band), plasmid vector (second from bottom), linear
Analysis and significance of results recombinant cut at only one of two cleavage sites (third
A considerable amount of sample variability is common from bottom), and open circular DNA (stippled band).
when learning to prepare miniscreen DNA. A typical gel Lane c. Digested plasmid DNA sample containing
with good quality DNA is illustrated below: undigested RNA (stippled region).
Lane d. Digested plasmid DNA sample contaminated with
digested bacterial chromosomal DNA not eliminated during
the DNA preparation.
Lane e. Unmelted agarose specks causing DNA streaking
and spots in the gel.
Lane f. Too much DNA loaded in the lane causing distortion
of bands.
Lane g. Bubble in sample well deforming DNA bands.
Lane h. Digested DNA sample degraded by contaminating
exonuclease or endonuclease.

Exercise 9. DNA fingerprinting

The ability to digest DNA fragments, separate these

fragments according to size, and detect fragments
containing specific genes has led to a genetic identification
84 Tait
approach called DNA fingerprinting. This method takes
advantage of the fact that a single nucleotide sequence
difference can cause the appearance or disappearance of
a restriction enzyme cleavage site in DNA. The individual-
specific differences in restriction enzyme cleavage site
position relative to a specific gene can cause variation in
the size of the DNA restriction fragment that carries that
gene in different individuals. The variation in the size of a
restriction fragment that carries a specific gene, referred
to as “restriction fragment length polymorphism” (RFLP),
can be used to genetically match DNA samples with the
donors from which they were obtained. Individuals who
appear identical for a specific physical trait can be easily
distinguished if sequence differences that cause changes
in DNA restriction fragment sizes are associated with that
trait.
When applied to identification of human DNA samples,
DNA fingerprint analysis is complicated by the presence
of hundreds or thousands of DNA fragments following
digestion of DNA samples with a specific restriction
enzyme. Rather than attempt to analyze all of the DNA
fragments, the fragments are generally separated by gel
electrophoresis, transferred to a membrane, and allowed
to react with a DNA or RNA hybridization probe that will
specifically anneal to a small number of the many different
DNA fragments. The probe fragment generally contains a
nucleoside that is either radioactive (such as 32PdATP) and
can be detected by autoradiography or has been modified
(such as biotinylated dATP) to be recognized by specific
antibodies and detected by a color reaction. The image
that is obtained by visualization of the probe is a subset of
the total set of DNA fragments and can be referred to as a
DNA fingerprint. When hybridization probes are chosen
carefully, the fingerprints can be specific for DNA that has
been found to have a high degree of individual-specific
variation. When sufficient information has been obtained
about the frequency of occurence of a specific DNA
fingerprint pattern, the DNA fingerprints of two DNA
samples can be used to calculate the probability of whether
the two DNA samples were obtained from the same
individual.
Since humans are diploid and contain two copies of
each chromosome, one from the mother and the other from
the father, a human DNA fingerprint can be thought of as
the combination of two fingerprint patterns. Since these
patterns can be used to link an “unknown” DNA sample to
DNA samples obtained from specific individuals, DNA
fingerprint analysis is becoming increasingly common as
courtroom evidence in paternity suits and in criminal
prosecution involving crimes like rape and murder. This
exercise will use bacteriophage lambda DNA digested with
various restriction enzymes to simulate the results of a DNA
fingerprint analysis and help determine paternity of a child.
Materials
Bacteriophage lambda DNA at a final concentration of 50
µg/ml in gel loading buffer, digested with the following
restriction enzymes: HindIII (H), EcoRI (E), BamHI (B), KpnI
(K), and SalI (S). Each of these digests will be used to
simulate a haploid DNA fingerprint (one set of
chromosomes). To make the test DNA samples obtained
from the individuals involved in the paternity suit, the
digested lambda DNA samples have been mixed in the
following manner to simulate the diploid chromosomal
fingerprint of each individual:
Mother = 100 µl H + 100 µl H (HH)
Baby = 100 µl H + 100 µl E (HE)
Rock Star = 100 µl H + 100 µl K (HK)
Ex-drummer = 100 µl S + 100 µl B (SB)
Mailman = 100 µl S + 100 µl E (SE)
Loading 7 µl of each mix will deliver 350 ng of DNA, giving
distinctive diploid DNA fingerprint patterns for each
individual.
• Gel box, gel tray and comb.
• Power supply.
• UV light source.
• Dry agarose.
• 10 mg/ml ethidium bromide.
• 10X TBE gel buffer.
Background
While living with a rock star, a young woman becomes
pregnant, whereupon the rock star promptly severs his
relationship with the woman, leaving her and the resultant
baby completely penniless. The mother of the child sues
for child support, claiming the rock star as the father of her
baby. The following are the summary statements from each
of the individuals who become involved in the resulting
paternity suit:
Mother: Rock Star is the father of my baby. He should
be required to financially support us.
Baby: Wah! Burp.
Rock Star: The child is not my son. The males in my
family were found through genetic analysis
to carry a recessive gene that causes
incurable craving for disco music. On the
advice of my doctor, I had a vasectomy when
I was twenty-three to prevent transmission
of this genetic disorder to my children. I
kicked her out because I caught her in bed
with my Drummer, not because she was
pregnant. She should talk to him about
support.
Ex-drummer: Who says I’m the father? I wasn’t the only
other guy she was seeing. I even caught the
mailman in the bedroom with her. I couldn’t
support her anyways. I can’t get work since
Rock Star kicked me out of his band and I
got busted with 2 pounds of heroin.
Mailman: Sure I was in her bedroom. I had a package
for Rock Star and needed a signature. When
I rang the doorbell, she called out she was
sick in bed, but the door was unlocked and
she would sign for the package if I didn’t
mind risking the flu. I was leaving her
bedroom when Drummer walked in the front
door. I think the door was unlocked and she
was in bed waiting for Drummer.
At the request of the court, DNA is extracted from blood
samples obtained from each of these individuals and
provided to you, who will perform the fingerprint analysis
and interpret the results.
 Introductory Experiments 85

Procedure Questions you will need to consider:

1. Weigh out 0.5 gram of the agarose and place in a 100
ml flask or beaker. Add 45 ml of distilled water and 5
ml of 10X TBE buffer.
2. Melt the agarose completely in a microwave oven or
boiling water bath. The solution must boil to melt the
agarose. Agarose has a tendency to superheat and
flash-boil, so be careful on the first boiling. The boiling
will be more controlled once some of the agarose has
melted. Be certain all the small particles are melted to
prevent streaks in the gel. The agarose should be
allowed to cool to about 55oC. It will solidify at about
45oC.
3. Add 2 µl of ethidium bromide to the agarose and mix.
This is the stain to detect the DNA. Ethidium bromide
is a mutagen (comparable to a pack of cigarettes) and
solutions containing ethidium should not be handled
with bare hands.
4. Pour a gel as demonstrated and allow to solidify.
5. Assemble the gel in the gel box. Submerge the gel in
1X TBE running buffer made by diluting 10 ml of 10X
TBE Buffer with 90 ml of distilled water.
6. Load the samples in the following order and amount:
Lane DNA Sample Amount
1. Is Rock Star the father of the Baby? Why or why not?
2. Is Drummer the father of the Baby? Why or why not?
3. Is Mailman the father of the Baby? Why or why not?
4. The probability that a DNA fingerprint will contain a
particular DNA band pattern is dependent on the
frequency of that particular band pattern in the general
population. You are now provided with the information
that the entire population of the USA has been
screened with the DNA probes you have just used and
the frequencies of occurrence of the H, E, K, B, and S
band patterns have been determined to be as follows:
Band pattern Frequency in population
H 1 in 100 people
E 1 in 10 people
K 1 in 100,000 people
B 1 in 100,000 people
S 1 in 50 people
Does this information change your answers to
questions 1-3 above, and why or why not?
5. As the court-appointed expert in DNA fingerprints, what
is your recommendation to the court regarding the
paternity suit and the identity of the father of the Baby?

1 Mother 7 µl Further Reading

2 Baby 7 µl
3 Rock Star 7 µl Tait, R.C. 1997. An Introduction to Molecular Biology.
4 Drummer 7 µl Horizon Scientific Press, Wymondham, UK.
5 Mailman 7 µl
6 Baby 7 µl

7. Plug in the leads and turn on the power. Voltage of

around 80 to 120 volts is typical, but will vary depending
on the gel box. A very low voltage will slow the run
down, but will enhance resolution of the DNA bands.
A very high voltage will heat the buffer and can actually
melt the gel. The depth of the buffer determines how
much current flows in the system. Use only enough
buffer to just submerge the gel to prevent excessive
heating of the gel (deep buffer = high current = high
heat production).
8. As the run progresses, two blue bands will resolve in
the gel. These are merely tracking dyes to judge how
far the DNA has migrated. When the faster dye is
reaches the bottom of the gel, turn off the power.
Remove the gel from the box and expose to the UV
light. Be careful to shield eyes and skin from the UV
light, as it is both a mutagen and a skin and eye burning
agent.
9. Either photograph or sketch the resulting band
patterns. Analyze the DNA band patterns. Remember
that the DNA fingerprint of each person will contain
two sets of bands, one from each parent. These could
be either two identical sets of bands, as in the case of
the Mother (HH), or two different sets of bands, as in
the case of the Baby (HE). The Mother must have
obtained one H set of bands from her mother and one
H set of bands from her father. The Baby must also
have obtained one set of bands from its mother and
one set from its father.
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